hca

metamodel version: 1.7.0

version: None

Classes

AggregateGenerationProtocol
AnalysisFile
AnalysisProcess
AnalysisProtocol
Barcode
BiologicalMacromoleculeOntology
BiomaterialCore
CellCycleOntology
CellLine
CellMorphology
CellSuspension
CellTypeOntology
CellularComponentOntology
Channel
CollectionProtocol
Contact
ContributorRoleOntology
Death
DevelopmentStageOntology
DifferentiationProtocol
DiseaseOntology
DissociationProtocol
DonorOrganism
EnrichmentOntology
EnrichmentProtocol
Entity
EthnicityOntology
FamilialRelationship
FileContentOntology
FileCore
FileDescriptor
FileFormatOntology
Funder
GrowthConditions
HumanSpecific
ImageFile
ImagedSpecimen
ImagingPreparationProtocol
ImagingProtocol
Input - An input to a process
InsdcExperiment
InstrumentOntology
IpscInductionProtocol
LengthUnitOntology
LibraryAmplificationOntology
LibraryConstructionOntology
LibraryPreparationProtocol
License
Links
MassUnitOntology
Matrix
MedicalHistory
MicroscopyOntology
MouseSpecific
OrganOntology
OrganPartOntology
Organoid
Output - An output from a process
Parameter
PlateBasedSequencing
PreservationStorage
Probe
Process
ProcessCore
ProcessLink
ProcessTypeOntology
Project
ProjectCore
Protocol
ProtocolCore
ProtocolReference - A protocol used in a process
ProtocolTypeOntology
Provenance
Publication
PurchasedReagents
ReferenceFile
S10x
SequenceFile
SequencingOntology
SequencingProtocol
SpeciesOntology
SpecimenFromOrganism
StateOfSpecimen
StrainOntology
SupplementaryFile
SupplementaryFileEntity
SupplementaryFileLink
TargetPathwayOntology
Task
TimeUnitOntology
Timecourse
TreatmentMethodOntology
TreatmentProtocol

Mixins

Slots

➞cell_uniformity - Description of the cell aggregates uniformity after formation.
➞describedBy - The URL reference to the schema.
➞formation_method - Method used to form cell aggregates.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞file_core - Core file-level information.
➞matrix_cell_count - Number of cells analyzed in a matrix file.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞analysis_run_type - Whether the analysis was run or was copied forward as an optimization.
➞describedBy - The URL reference to the schema.
➞inputs
➞process_core - Core process-level information.
➞provenance - Provenance information provided by the system.
➞reference_files
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞tasks
➞timestamp_start_utc - Initial start time of the full pipeline in UTC.
➞timestamp_stop_utc - Terminal stop time of the full pipeline in UTC.
➞type - The type of process.
➞computational_method - A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository.
➞describedBy - The URL reference to the schema.
➞matrix - Information related to protocols that output a matrix.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞type - The type of protocol.
➞barcode_length - Length of barcode in nucleotides.
➞barcode_offset - The 0-based offset of start of barcode in read.
➞barcode_read - The read in which the barcode is found.
➞describedBy - The URL reference to the schema.
➞schema_version - The version number of the schema in major.minor.patch format.
➞white_list_file - Name of file containing legitimate barcode sequences.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of the biological macromolecule being used.
➞HDBR_accession - A Human Developmental Biology Resource (HDBR) sample accession.
➞biomaterial_description - A general description of the biomaterial.
➞biomaterial_id - A unique ID for the biomaterial.
➞biomaterial_name - A short, descriptive name for the biomaterial that need not be unique.
➞biosamples_accession - A BioSamples accession.
➞describedBy - The URL reference to the schema.
➞genotype - Genotype of the biomaterial.
➞insdc_sample_accession - An International Nucleotide Sequence Database Collaboration (INSDC) sample accession.
➞ncbi_taxon_id
➞schema_version - The version number of the schema in major.minor.patch format.
➞supplementary_files
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The name of a cell cycle of the cells in the specimen.
➞biomaterial_core - Core biomaterial-level information.
➞catalog_number - The supplier catalogue number for the cell line.
➞catalog_url - The supplier catalogue URL for the cell line.
➞cell_cycle - The cell cycle phase if the cell line is synchronized growing cells or the phase is known.
➞cell_morphology - Features relating to the morphology of the cells.
➞cell_type - The cell type that the cell line represents.
➞confluency - The percent a plate surface is covered by cells.
➞date_established - Date when the cell line was established.
➞describedBy - The URL reference to the schema.
➞disease - Short description of any disease association to the cell type.
➞genus_species
➞growth_conditions - Features relating to the growth and/or maintenance of the cell lines.
➞karyotype - The karyotype of the cell line.
➞lot_number - The supplier lot or batch number for the cell line.
➞model_organ - Organ for which this cell line is a model.
➞provenance - Provenance information provided by the system.
➞publication - A publication that cites the cell line creation.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞supplier - The supplier of the cell line.
➞timecourse - Information relating to a timecourse associated with this cell line.
➞tissue - The tissue that the cell line was derived from.
➞type - The type of cell line.
➞cell_morphology - General description of the morphology of cells.
➞cell_size - Size of cells in Cell size unit.
➞cell_size_unit - The unit in which the Cell size is expressed.
➞cell_viability_method - The method by which cell viability was determined.
➞cell_viability_result - Result of the cell viability test.
➞describedBy - The URL reference to the schema.
➞percent_cell_viability - Percent of cells determined to be viable.
➞percent_necrosis - Percent of cells identified to be necrotic.
➞schema_version - The version number of the schema in major.minor.patch format.
➞biomaterial_core - Core biomaterial-level information.
➞cell_morphology - Features relating to the morphology of cells in a biomaterial.
➞describedBy - The URL reference to the schema.
➞estimated_cell_count - Estimated number of cells in the suspension.
➞genus_species
➞growth_conditions - Features relating to the growth and/or maintenance of a biomaterial.
➞plate_based_sequencing - Fields specific for plate-based sequencing experiments.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞selected_cell_types
➞timecourse - Information relating to a timecourse associated with this cell suspension.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The name of a cell type supplied by a user.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a subcellular structure.
➞channel_id - User given ID. If there is an accompanying codebook, this name should correspond to the channel id used in the codebook.
➞describedBy - The URL reference to the schema.
➞excitation_wavelength - Excitation wavelength of the lightsource in nanometers.
➞exposure_time - Acquisition time for a single image per channel, in milliseconds.
➞filter_range - Emission filter in nanometers.
➞multiplexed - Whether multiple targets were detected simultaneously in this channel.
➞schema_version - The version number of the schema in major.minor.patch format.
➞target_fluorophore - The name of the fluorophore this channel is designed to assay.
➞describedBy - The URL reference to the schema.
➞method - Method used to collect the biomaterial.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞reagents
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞address - Street address where the individual works.
➞corresponding_contributor - Whether the individual is a primary point of contact for the project.
➞country - Country where the individual works.
➞describedBy - The URL reference to the schema.
➞email - Email address for the individual.
➞institution - Name of primary institute where the individual works.
➞laboratory - Name of lab or department within the institute where the individual works.
➞orcid_id - The individual's ORCID ID linked to previous work.
➞phone - Phone number of the individual or their lab.
➞project_role - Primary role of the individual in the project.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The primary role of the contributor in the project.
➞cause_of_death - Conditions resulting in death.
➞cold_perfused - Whether perfusion with cold fluid was used to help preserve tissues before heart stopped.
➞days_on_ventilator - Number of days on ventilator before death occurred.
➞describedBy - The URL reference to the schema.
➞hardy_scale - Value on 4-point Hardy scale cause of death classification.
➞normothermic_regional_perfusion - Whether entire body was perfused with warm oxygenated blood.
➞organ_donation_death_type - Type of death preceding organ donation.
➞schema_version - The version number of the schema in major.minor.patch format.
➞time_of_death - Date and time when death was declared.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The name of the development stage of the organism.
➞describedBy - The URL reference to the schema.
➞media - Culture media used to induce a specific differentiation response.
➞method - Method applied to cell culture to induce a specific differentiation response.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞reagents
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞small_molecules - Small molecules added to stem cell medium to induce a specific differentiation response.
➞target_cell_yield - Percent of target cells obtained after directed differentiation of origin cell.
➞target_pathway - Targeted pathway for specific differentiation response.
➞validation_method - Method used to validate origin cell successfully differentiated to target cell.
➞validation_result - Result confirming successful differentiation to target cell type.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The text for the term as the user provides it.
➞describedBy - The URL reference to the schema.
➞method - How cells or organelles were dissociated.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞reagents
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞biomaterial_core - Core biomaterial-level information.
➞death - Information about conditions of death of the organism.
➞describedBy - The URL reference to the schema.
➞development_stage - A classification of the developmental stage of the organism.
➞diseases
➞familial_relationships
➞genus_species
➞gestational_age - Gestational age of pregnancy in Gestational age units measured from the last menstrual period.
➞gestational_age_unit - The unit in which Gestational age is expressed.
➞height - Height of organism in Height unit.
➞height_unit - The unit in which Height is expressed.
➞human_specific - Fields specific to human (homo sapiens) organisms.
➞is_living - Whether organism was alive at time of biomaterial collection.
➞medical_history - Information about the medical history of the organism.
➞mouse_specific - Fields specific to mouse (mus musculus) organisms.
➞organism_age - Age of organism in Age units measured since birth.
➞organism_age_unit - The unit in which Age is expressed.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞sex - The biological sex of the organism.
➞timecourse - Information relating to a timecourse associated with this biomaterial.
➞weight - Weight of organism in Weight unit.
➞weight_unit - The unit in which Weight is expressed.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of an enrichment approach being used.
➞describedBy - The URL reference to the schema.
➞markers - A list of markers used to enrich for or against certain cells.
➞maximum_size - Maximum cell or organelle size passing selection, in microns.
➞method - The method by which enrichment was achieved.
➞minimum_size - Minimum cell or organelle size passing selection, in microns.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞entity_id - ID of this entity
➞entity_type - The concrete type of this entity
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The ethnicity of the human donor.
➞child - The individual's child.
➞describedBy - The URL reference to the schema.
➞parent - The individual's parent.
➞schema_version - The version number of the schema in major.minor.patch format.
➞sibling - The individual's sibling.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - General description of the contents of the file.
➞checksum - MD5 checksum of the file.
➞content_description
➞describedBy - The URL reference to the schema.
➞file_name - The name of the file.
➞file_source - The source of the file. This is typically an organisation, repository, person or dedicated process.
➞format - The format of the file.
➞schema_version - The version number of the schema in major.minor.patch format.
➞content_type - An appropriate MIME type for this file.
➞crc32c - The CRC-32C code generated for this file.
➞describedBy - The URL reference to the schema.
➞file_id - UUID that uniquely identifies each data file in its source
➞file_name - The object name of the data file relative to the staging area's data/ directory
➞file_version - The version of the file given in date time format
➞s3_etag - An AWS S3 ETag of this file
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞sha1 - The SHA-1 hash of the file.
➞sha256 - The SHA-256 hash of the file.
➞size - The size of the file in bytes.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of the file format.
➞describedBy - The URL reference to the schema.
➞grant_id - The unique grant identifier or reference.
➞grant_title - The name of the grant funding the project.
➞organization - The name of the funding organization.
➞schema_version - The version number of the schema in major.minor.patch format.
➞culture_environment - Cell culture environment in which cells are grown.
➞describedBy - The URL reference to the schema.
➞drug_treatment - Description of drugs added to the growth medium.
➞feeder_layer_type - Type of feeder layer cells on which biomaterial was grown.
➞growth_medium - The solid, liquid, or semi-solid medium used to support growth.
➞mycoplasma_testing_method - The method by which the biomaterial was tested for mycoplasma contamination.
➞mycoplasma_testing_results - Whether the biomaterial passed or failed the mycoplasma test.
➞passage_number - The number of passages that the biomaterial has been through.
➞schema_version - The version number of the schema in major.minor.patch format.
➞body_mass_index - The body mass index of the donor.
➞describedBy - The URL reference to the schema.
➞ethnicity
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞file_core - Core file-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞biomaterial_core - Core biomaterial-level information.
➞describedBy - The URL reference to the schema.
➞internal_anatomical_structures
➞overview_images
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞slice_thickness - Thickness of the imaged slice in micrometres.
➞describedBy - The URL reference to the schema.
➞expansion_factor - Factor by which the imaged tissue was expanded in one dimension.
➞fiducial_marker - Fiducial markers for the alignment of images taken across multiple rounds of imaging.
➞final_slicing_method - The method by which the final slice was obtained.
➞fresh_slicing_method - The method by which fresh tissue was sliced.
➞imaged_slice_thickness - Thickness of the imaged slice in micrometres.
➞permeabilisation_time - The permeabilisation time in time units that the tissue was exposed to.
➞permeabilisation_time_unit - The unit in which permeabilisation time is expressed.
➞post_final_slicing_interval - Length of time between secondary slicing and hybridization.
➞post_final_slicing_interval_unit - The unit of time in which the post final slicing interval is expressed.
➞post_resection_interval - Length of time between surgical resection and fresh slicing of tissue.
➞post_resection_interval_unit - The unit of time in which the post resection interval is expressed.
➞pre_final_slice_preservation_method - Tissue preservation method used prior to final slicing.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞channel
➞describedBy - The URL reference to the schema.
➞immersion_medium_refractive_index - Refractive index of the immersion medium used for imaging.
➞immersion_medium_type - Immersion medium used for imaging.
➞magnification - Magnification of the objective used for imaging.
➞microscope_setup_description - Description of the microscope setup.
➞microscopy_technique - The type of microscopy.
➞number_of_tiles - Number of XY tiles in the experiment.
➞number_of_z_steps - Number of steps in a Z stack.
➞numerical_aperture - Numerical aperture of the objective.
➞overlapping_tiles - Whether tiles were collected with overlap.
➞pixel_size - Pixel size in nanometers.
➞probe
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞tile_size_x - X size of the tile in micrometers.
➞tile_size_y - Y size of the tile in micrometers.
➞z_stack_step_size - Z-stack step size in nanometers.
➞input_id - UUID of the input entity.
➞input_type - The concrete type of the input entity.
➞describedBy - The URL reference to the schema.
➞insdc_experiment_accession - An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The full name of the instrument used.
➞describedBy - The URL reference to the schema.
➞ipsc_induction_kit - Kit used to induce pluripotent stem cell generation.
➞method - Induction method applied to primary cell culture to induce pluripotent stem cell generation.
➞percent_pluripotency - Percent of iPSCs that passed the pluripotency test.
➞pluripotency_test - Description of how pluripotency was tested in induced pluripotent stem cells.
➞pluripotency_vector_removed - Whether a viral vector was removed after induction.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞reagents
➞reprogramming_factors - Reprogramming factors added to primary cell culture to induce pluripotency.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a length unit being used.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a library amplification approach being used.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a library construction approach being used.
➞cdna_library_amplification_method - The method used to amplify cDNA library prior to sequencing.
➞cell_barcode - Information about cell identifier barcodes.
➞describedBy - The URL reference to the schema.
➞end_bias - The type of tag or end bias the library has.
➞input_nucleic_acid_molecule - Starting nucleic acid molecule isolated for sequencing.
➞library_construction_kit - Name of kit used to construct the sequencing library.
➞library_construction_method - The general method for sequencing library construction.
➞library_preamplification_method - The method used to amplify RNA prior to adaptor ligation.
➞nominal_length - Average (insert) size of the fragments being sequenced.
➞nominal_sdev - Standard deviation of the (insert) size of the fragments being sequenced.
➞nucleic_acid_conversion_kit - Name of kit used to convert RNA to DNA for sequencing.
➞nucleic_acid_source - Source cells or organelles from which nucleic acid molecules were collected.
➞primer - Primer used for cDNA synthesis from RNA.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞spatial_barcode - Information about spatial barcodes.
➞spike_in_dilution - Dilution of spike-in.
➞spike_in_kit - Information about a spike-in kit.
➞strand - Library strandedness.
➞umi_barcode - Information about unique molecular identifier (UMI) barcodes.
➞describedBy - The URL reference to the schema.
➞full_name - Full name of the license under which this dataset is made available.
➞identifier - Identifier of the license under which this dataset is made available.
➞schema_version - The version number of the schema in major.minor.patch format.
➞url - URL of the license under which this data is available.
➞describedBy - The URL reference to the schema.
➞links
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a mass unit being used.
➞data_normalization_methods
➞derivation_process
➞describedBy - The URL reference to the schema.
➞schema_version - The version number of the schema in major.minor.patch format.
➞alcohol_history - Estimated amount of alcohol consumed per day.
➞describedBy - The URL reference to the schema.
➞medication - Medications the individual was taking at time of biomaterial collection.
➞nutritional_state - Nutritional state of individual at time of biomaterial collection.
➞schema_version - The version number of the schema in major.minor.patch format.
➞smoking_history - Estimated number of cigarettes smoked per day.
➞test_results - Results from medical tests performed on the individual.
➞treatment - Treatments the individual has undergone prior to biomaterial collection.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - Version number in major.minor.patch format.
➞text - The name of the type of microscopy used in an imaging experiment.
➞describedBy - The URL reference to the schema.
➞schema_version - The version number of the schema in major.minor.patch format.
➞strain
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The text for the term as the user provides it.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The text for the term as the user provides it.
➞age - Age of the organoid in Organoid age unit measured from when cell aggregates started differentiating to desired organoid model.
➞age_unit - The unit in which Organoid age is expressed.
➞biomaterial_core - Core biomaterial-level information.
➞describedBy - The URL reference to the schema.
➞embedded_in_matrigel - Whether the organoid is embedded in a matrigel.
➞genus_species
➞growth_environment - Growth environment in which the organoid is grown.
➞input_aggregate_cell_count - Estimated number of cells per input cell aggregate.
➞model_organ - Organ for which this organoid is a model system.
➞model_organ_part - Organ part for which this organoid is a model system.
➞morphology - General description of the organoid morphology.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞size - Size of the organoid in Organoid size unit.
➞size_unit - The unit in which the Organoid size is expressed.
➞stored_oxygen_levels - Percent oxygen level organoid was stored in prior to sequencing.
➞output_id - UUID of the output entity.
➞output_type - The concrete type of the output entity.
➞checksum - MD5 checksum of the file.
➞parameter_name - Name of parameter.
➞parameter_value - Path to file for or value of parameter.
➞describedBy - The URL reference to the schema.
➞plate_label - A label or name for the plate on which the well is located.
➞schema_version - The version number of the schema in major.minor.patch format.
➞well_label - A label or name for the well in which the cell is located.
➞well_quality - Quality of well if imaged before sequencing.
➞describedBy - The URL reference to the schema.
➞preservation_method - The method by which a biomaterial was preserved through the use of chemicals, cold, or other means to prevent or retard biological or physical deterioration.
➞schema_version - The version number of the schema in major.minor.patch format.
➞storage_method - The method by which a biomaterial was stored after preservation or before another protocol was used.
➞storage_time - Length of time the biomaterial was stored for in Storage time units.
➞storage_time_unit - The unit in which Storage time is expressed.
➞assay_type - Type of assay used to detect target.
➞channel_label
➞describedBy - The URL reference to the schema.
➞fluorophore
➞probe_label - The label of a probe used to detect target in this experiment.
➞probe_reagents - Name of reagents used to construct the probe.
➞probe_sequence - Sequence of a probe used to detect target.
➞schema_version - The version number of the schema in major.minor.patch format.
➞subcellular_structure - Target subcellular structure.
➞target_codebook_label - A label used in the codebook for the target.
➞target_label - An identifier for the target molecule.
➞target_name - The name of the target molecule.
➞describedBy - The URL reference to the schema.
➞location - Location where the process took place.
➞operators
➞process_description - A general description of the process.
➞process_id - A unique ID for the process.
➞process_name - A short, descriptive name for the process that need not be unique.
➞schema_version - The version number of the schema in major.minor.patch format.
➞inputs
➞link_type - The type of this link.
➞outputs
➞process_id - UUID of the process described by this link.
➞process_type - The concrete type of the process described by this link.
➞protocols
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a process type being used.
➞describedBy - The URL reference to the schema.
➞deviation_from_protocol - A deviation from the protocol provided.
➞end_time - Date and time the process ended.
➞insdc_experiment - An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession.
➞length_of_time - Length of time the process took to execute in Length of time unit.
➞length_of_time_unit - The unit in which Length of time is expressed.
➞process_core - Core process-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞start_time - Date and time the process started.
➞type - The type of process.
➞describedBy - The URL reference to the schema.
➞project_description - A longer description of the project which includes research goals and experimental approach.
➞project_short_name - A short name for the project.
➞project_title - An official title for the project.
➞schema_version - The version number of the schema in major.minor.patch format.
➞array_express_accessions
➞biostudies_accessions
➞contributors
➞dbgap_accessions
➞describedBy - The URL reference to the schema.
➞ega_accessions
➞estimated_cell_count - An estimated number of cells in this project
➞funders
➞geo_series_accessions
➞insdc_project_accessions
➞insdc_study_accessions
➞project_core - Core project-level information.
➞provenance - Provenance information provided by the system.
➞publications
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞supplementary_links
➞describedBy - The URL reference to the schema.
➞document - A filename of a PDF document containing the details of the protocol.
➞protocol_description - A general description of the protocol.
➞protocol_id - A unique ID for the protocol.
➞protocol_name - A short name for the protocol.
➞protocols_io_doi - The protocols.io digital object identifier (doi) for the protocol.
➞publication_doi - The publication digital object identifier (doi) for the protocol.
➞schema_version - The version number of the schema in major.minor.patch format.
➞protocol_id - UUID of the protocol entity.
➞protocol_type - The concrete type of protocol entity.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a protocol type used.
➞describedBy - The URL reference to the schema.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞type - The type of protocol.
➞accession - A unique accession for this entity, provided by the broker.
➞describedBy - The URL reference to the schema.
➞document_id - Identifier for document.
➞schema_major_version - The major version number of the schema.
➞schema_minor_version - The minor version number of the schema.
➞schema_version - The version number of the schema in major.minor.patch format.
➞submission_date - When project was first submitted to database.
➞submitter_id - ID of individual who first submitted project.
➞update_date - When project was last updated.
➞updater_id - ID of individual who last updated project.
➞authors
➞describedBy - The URL reference to the schema.
➞doi - The publication digital object identifier (doi) of the publication.
➞official_hca_publication - Has the publication been accepted as an official HCA publication, according to the process described in https://www.humancellatlas.org/publications/ ?
➞pmid - The PubMed ID of the publication.
➞schema_version - The version number of the schema in major.minor.patch format.
➞title - The title of the publication.
➞url - A URL for the publication.
➞catalog_number - The catalog number of the kit/reagent.
➞describedBy - The URL reference to the schema.
➞expiry_date - The date of expiration for the kit/reagent.
➞kit_titer - Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis.
➞lot_number - The batch or lot number of the kit/reagent.
➞manufacturer - The manufacturer of the kit/reagent.
➞retail_name - The retail name of the kit/reagent.
➞schema_version - The version number of the schema in major.minor.patch format.
➞assembly_type - The assembly type of the genome reference file.
➞describedBy - The URL reference to the schema.
➞file_core - Core file-level information.
➞genus_species - The scientific binomial name for the species of this reference.
➞ncbi_taxon_id - A taxonomy ID (taxonID) from NCBI.
➞provenance - Provenance information provided by the system.
➞reference_type - The type of the reference file.
➞reference_version - The genome version of the reference file.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞drop_uniformity - Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run.
➞fastq_method - Method used for the generation of fastq files from bcl files.
➞fastq_method_version - Version of the program used for fastq generation.
➞pooled_channels - The number of channels pooled within a sequencing lane.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞file_core - Core file-level information.
➞insdc_run_accessions
➞lane_index - The lane that this file was sequenced from.
➞library_prep_id - A unique ID for the library preparation.
➞provenance - Provenance information provided by the system.
➞read_index - The sequencing read this file represents.
➞read_length - The length of a sequenced read in this file, in nucleotides.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a sequencing approach being used.
➞describedBy - The URL reference to the schema.
➞instrument_manufacturer_model - The manufacturer and model of the sequencer.
➞local_machine_name - Local name for the particular machine used for sequencing.
➞method - The general method for sequencing.
➞paired_end - Whether the sequenced molecule was sequenced from both ends.
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞s10x - Fields specific for 10x experiments.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of the species to which the organism belongs.
➞biomaterial_core - Core biomaterial-level information.
➞collection_time - When the biomaterial was collected.
➞describedBy - The URL reference to the schema.
➞diseases
➞genus_species
➞organ - The organ that the biomaterial came from.
➞organ_parts
➞preservation_storage - Information about how a specimen was preserved and/or stored over a period of time.
➞provenance - Provenance information provided by the system.
➞purchased_specimen - Information about a purchased specimen.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞state_of_specimen - State of the specimen at the time of collection.
➞autolysis_score - State of tissue breakdown due to self-digestion.
➞describedBy - The URL reference to the schema.
➞gross_description - Color, size, and other aspects of specimen as visible to naked eye.
➞gross_images
➞ischemic_temperature - Whether specimen experienced warm or cold ischemia.
➞ischemic_time - Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed.
➞microscopic_description - How the specimen looks under the microscope and how it compares with normal cells.
➞microscopic_images
➞postmortem_interval - Duration of time between when death was declared and when the specimen was preserved or processed.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of the strain to which the organism belongs.
➞file_id - ID for this supplementary file entity
➞file_type - concrete type of this supplementary file entity
➞entity - An entity that refers to this supplementary file
➞files
➞link_type - The type of this link.
➞describedBy - The URL reference to the schema.
➞file_core - Core file-level information.
➞file_description - A short description of the file contents.
➞provenance - Provenance information provided by the system.
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of the treatment target pathway.
➞cpus - Number of CPUs used to run this task.
➞disk_size - Name of the disk volume mounted to the VM for the task.
➞docker_image - Name of docker image where the task is stored and executed.
➞log_err - Path where standard error is logged.
➞log_out - Path where standard output is logged.
➞memory - Amount of memory allocated for this task.
➞start_time - Date and time when the task started.
➞stop_time - Date and time when the task finished.
➞task_name - Name of the task.
➞zone - Name of the Google Cloud zone where the task was run.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a time unit being used.
➞describedBy - The URL reference to the schema.
➞relevance - Relevance of the Timecourse value/unit to the experiment.
➞schema_version - The version number of the schema in major.minor.patch format.
➞unit - The unit in which the Timecourse value is expressed.
➞value - The numerical value in Timecourse unit associated with a time interval used in the experiment.
➞describedBy - The URL reference to the schema.
➞ontology - An ontology term identifier in the form prefix:accession.
➞ontology_label - The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.
➞schema_version - The version number of the schema in major.minor.patch format.
➞text - The name of a treatment method or approach being used.
➞describedBy - The URL reference to the schema.
➞media - Culture media used to induce a specific treatment response.
➞method
➞protocol_core - Core protocol-level information.
➞provenance - Provenance information provided by the system.
➞reagents
➞schema_type - The type of the metadata schema entity.
➞schema_version - The version number of the schema in major.minor.patch format.
➞target_pathway

Enums

Subsets

Types

Built in

Bool
Decimal
ElementIdentifier
NCName
NodeIdentifier
URI
URIorCURIE
XSDDate
XSDDateTime
XSDTime
float
int
str

Defined

Boolean (Bool) - A binary (true or false) value
Date (XSDDate) - a date (year, month and day) in an idealized calendar
DateOrDatetime (str) - Either a date or a datetime
Datetime (XSDDateTime) - The combination of a date and time
Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
Double (float) - A real number that conforms to the xsd:double specification
Float (float) - A real number that conforms to the xsd:float specification
Integer (int) - An integer
Ncname (NCName) - Prefix part of CURIE
Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
String (str) - A character string
Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
Uri (URI) - a complete URI
Uriorcurie (URIorCURIE) - a URI or a CURIE